DOI: 10.18129/B9.bioc.DEXSeq    

Inference of differential exon usage in RNA-Seq

Bioconductor version: Release (3.6)

The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.

Author: Simon Anders <sanders at> and Alejandro Reyes <alejandro.reyes.ds at>

Maintainer: Alejandro Reyes <alejandro.reyes.ds at>

Citation (from within R, enter citation("DEXSeq")):


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PDF R Script Analyzing RNA-seq data for differential exon usage with the "DEXSeq" package
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biocViews AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, RNASeq, Sequencing, Software, Visualization
Version 1.24.3
In Bioconductor since BioC 2.9 (R-2.14) (6.5 years)
License GPL (>= 3)
Depends BiocParallel, Biobase, SummarizedExperiment, IRanges(>= 2.5.17), GenomicRanges(>= 1.23.7), DESeq2(>= 1.9.11), AnnotationDbi, RColorBrewer, S4Vectors
Imports BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools, statmod, geneplotter, genefilter
Suggests GenomicFeatures(>= 1.13.29), pasilla(>= 0.2.22), parathyroidSE, BiocStyle, knitr
Depends On Me
Imports Me IntEREst
Suggests Me GenomicRanges, JctSeqData, oneChannelGUI, pasilla, stageR, subSeq
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